If you have very many, it will probably be a tedious and frustrating process at this point, as the bookmark manager still has a long way to go to become a powerful, useful sorting tool. Once you get them sorted adding new ones where you want works fairly well by selecting the folder you want when you create a new bookmark using the standard Ctrl+D shortcut.

For now, open a Speed Dial and click on the Bookmarks button to open the Bookmarks Manager. There you can create/edit/delete new folders or bookmarks and drag bookmarks and folders to rearranged them. But it is very difficult to drag a bookmark over a closed folder without the folder popping open almost instantly, hence one of the challenges of sorting if you have very many to sort.